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Friday, September 28, 2012

read.simmap: computation time rises more than linearly with the number of trees

Sam Price reports that computation time for phytools function read.simmap(...,version=1.5) rises more than linearly with the number of trees in the input file. That means that it takes (substantially) more than twice as long to read in a data file containing 200 trees than it does to read in a data file containing 100 trees. (Or, equivalently, it would be faster to split your trees into two files and then read them in separately.)

Well, it turns out that Sam is right, of course - but I haven't yet figured out why. If I have time, I will try and figure this out tomorrow. Here is the result of reading in tree files with various numbers of trees using read.simmap and timing the result using system.time (if it seems slow it is because I am running it on my VAIO ultrabook):

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About this blog

This web-log chronicles the development of new tools for phylogenetic analyses in the phytools R package. Unless you a reading a very recent page of the blog, I recommend that you install the latest CRAN version of phytools (or latest beta release) before attempting to replicate any of the analyses of this site. That is because the linked functions may be archived, and very likely have been replaced by newer versions.